Phalaris Pre-Breeding

Summary

Phalaris (Phalaris aquatica) is an important perennial grass sown for meat production in temperate Australia.  The species has a reputation for being persistent and able to support high levels of animal production. In contrast to species such as perennial ryegrass where major efforts have been undertaken to develop genetic and genomic technologies to increase the rate of genetic gain in the species, genetic research in Phalaris has focussed in recent decades on the development of new cultivars to address requirements of farming systems such as winter-activity, aluminium tolerance and grazing tolerance.

The main purpose of this project was to describe new pre-breeding traits and develop breeding technologies for the phalaris species that will enable the rate of genetic gain in phalaris breeding programs to be increased.

Three work packages (sets of discrete activities for delivery of a program sub-component) of co-ordinated activities will contribute to the development of tools and technologies to increase the rate of genetic gain in phalaris breeding programs and will achieve the following outcomes:

• Genetic gain in phalaris described and quantified in economic terms
• Phalaris breeding programs prepared for genomics assisted breeding strategies
• The use of phalaris as a model for the deployment of improved breeding

The following objectives were delivered:

1. Described the phenotypic and genetic diversity in phalaris (bred both within Australia and internationally) germplasm to guide the design of future breeding programs, with a focus on the winter-active germplasm pools including the development of molecular marker panels suitable for cultivar identification and genetic diversity studies.  These pools had been identified as priority areas for further breeding based on consultations with seed companies.
2. Developed a methodology for genomic selection for complex traits such as yield and persistence (based on the regression of allelic variation in genetic markers with phenotypic variability) in phalaris breeding programs, in collaboration with private seed companies, which will allow for more efficient selection of quantitative traits relevant to the economic value of phalaris. The most economically important traits of total yield and seasonal yield distribution were used in the model.
3. Developed markers for seed retention as a mechanism to increase the rate of genetic gain in phalaris breeding programs.
4. Used economic analyses to develop robust estimates of the economic importance of genetic gain in phalaris in red meat production systems that can be used toAssess the genetic merit of individual plants and cultivars.Assess the value of individual sub-traits (such as pest and disease tolerance) that contribute to pasture traits such as seasonal yield and persistence.Calculate the economic benefit of new sowings to producers.
5. Private seed companies using these technologies (genomic selection methodologies, gene markers for seed retention, genetic diversity analyses) in their own breeding programs. 

As a result of this project more than 140,000,000 bp of reference data have been sequenced from the phalaris genome and more than 500,000 putative SNPs identified at a frequency of 1 SNP per 262 bp. This is by far the largest contribution of phalaris sequence information and will act as a resource for further research and practical outcomes in phalaris breeding.

An economic model to assess differences in the value of phalaris has been developed based on the relative importance of seasonal yield and could be used as the basis of a genomic selection program.  This information could also be combined with cultivar evaluation data from the Pasture Trial Network (PTN) to develop a Forage Value Index for phalaris cultivars similar to that which has been successfully released for perennial ryegrass cultivars for the dairy industry.

Proof of concept of the use of genomic information to select for yield and seed characteristics has been obtained.Lessons/ key messagesPopulation structure in phalaris germplasm means that the initial application of genomic selection methods will require that reference populations are developed based on the diversity analysis within this project.  This situation is analogous to 'within breed' vs 'across breed' selection models in cattle.

Depending on company relationships and breeding priorities there is the opportunity to pool resources during the development and evaluation of reference populations.

Genomic sequence information can be used to accurately identify phalaris cultivars.

The use of economic weightings to measure the economic value of genetic gain and the relative importance of seasonal production in meat production systems could be used to develop a "Breeding Objective" for use in selection that would be aligned with a "Forage Value Index" used in cultivar evaluation that would integrate selection and measurement throughout the genetics supply chain.